c4cam / musica

MuSiCa - Mutational Signatures in Cancer

MuSiCa - Mutational Signatures in Cancer

MuSiCa (Mutational Signatures in Cancer) is a shiny-based web application aimed to visualize the somatic mutational profile of a series of provided samples (different formats are allowed) and to extract the contribution of the reported mutational signatures (Alexandrov L.B. et al., Nature (2013), Catalogue Of Somatic Mutations In Cancer, COSMIC (2017)) on their variation profile. It is mainly based on the MutationalPatterns R package (Blokzijl et al., Genome Medicine (2018)).

Please give credit and cite MuSiCa app when you use it for your genomic analysis (Díaz-Gay et al., BMC Bioinformatics (2018)).

Running the app

There are many ways to download and run Mutational Signatures ShinyApp:

First check the dependencies (you only need to do this once):

if(!require(MutationalPatterns)) {source("http://www.bioconductor.org/biocLite.R");biocLite("MutationalPatterns")}
if(!require(VariantAnnotation)) {source("http://www.bioconductor.org/biocLite.R");biocLite("VariantAnnotation")}
if(!require(BSgenome.Hsapiens.UCSC.hg38)) {source("http://www.bioconductor.org/biocLite.R");biocLite("BSgenome.Hsapiens.UCSC.hg38")}
if(!require(BSgenome.Hsapiens.UCSC.hg19)) {source("http://www.bioconductor.org/biocLite.R");biocLite("BSgenome.Hsapiens.UCSC.hg19")}
if(!require(BSgenome.Hsapiens.1000genomes.hs37d5)) {source("http://www.bioconductor.org/biocLite.R");biocLite("BSgenome.Hsapiens.1000genomes.hs37d5")}

if(!require(ggplot2)) install.packages("ggplot2")
if(!require(heatmaply)) install.packages("heatmaply")
if(!require(gplots)) install.packages("gplots")
if(!require(reshape2)) install.packages("reshape2")
if(!require(data.table)) install.packages("data.table")
if(!require(readxl)) install.packages("readxl")
if(!require(openxlsx)) install.packages("openxlsx")

if(!require(shiny)) install.packages("shiny")
if(!require(shinyBS)) install.packages("shinyBS")
if(!require(devtools)) install.packages("devtools")
if(!require(shinysky)) {library(devtools); devtools::install_github("AnalytixWare/ShinySky")}
if(!require(shinyjs)) install.packages("shinyjs")
if(!require(V8)) install.packages("V8")
if(!require(shinythemes)) install.packages("shinythemes")
if(!require(plotly)) install.packages("plotly")
if(!require(webshot)) install.packages("webshot")
webshot::install_phantomjs()

Then load the shiny app:

library(shiny)

# Easiest way is to use runGitHub
runGitHub("musica", "marcos-diazg")

Other ways to load the app:

# Run a tar or zip file directly
runUrl("https://github.com/marcos-diazg/musica/archive/master.tar.gz")
runUrl("https://github.com/marcos-diazg/musica/archive/master.zip")

# Using runApp(),  first clone the repository with git. If you have cloned it into
# ~/music, first go to that directory, then use runApp().
setwd("~/musica")
runApp()